Improve documentation

[grst]

In GitLab by @grst on Mar 20, 2020, 18:35

• citations are not rendered correctly atm.

API docs

In particular, double-check all docstrings for

• correct formatting
• completeness
• understandabliness (does that work even exist?)
• proper citation of other methods

At that occation:

• make sure all functions have sensible default parameters

General documentation

• data structure (scirpy.read_10x_vdj(path, filtered=True) #121 )
• Explain API doc (consistent with scanpy, what are tools, pp tools etc.)
• Page "usage principles" -> can include the data structure and a section on how to import data.
• add sample images for plotting functions
• Go through tutorial to reflect changes of docs.

[grst]

In GitLab by @grst on Mar 20, 2020, 18:37

changed the description

[grst]

In GitLab by @grst on Apr 6, 2020, 17:15

changed the description

[grst]

In GitLab by @grst on Apr 7, 2020, 17:24

Include overview figure from the paper in README

Figure 1: The scirpy workflow. After defining clonotypes via CDR3-sequence similarity, scirpy offers a wide range of visualization options to explore clonotype expansion, abundance and VDJ gene usage. Finally, clonotype information can be integrated with transcriptomics data, leveraging the scanpy workflow. Top panel: Exemplary clonotype network. Each node represents a cell, colored by sample. Edges connect cells belonging to the same clonotype. Middle panel: Clonal expansion visualized as bar chart. The bars colored in blue, orange and green represent the fractions of cells belonging to clonotypes with one, two or more than two cells, respectively. Lower panel: UMAP embedding based on gene expression. Cells belonging to the twelve most abundant clonotypes are highlighted in color.

[grst]

All todos have been addressed in #124 or been migrated into their own issues.